


Freedom and Choices

by SolaraMoonset



Category: Star Trek, Star Trek: Alternate Original Series (Movies)
Genre: F/M, Family Secrets, Not your average love story, Slow Burn
Language: English
Status: In-Progress
Published: 2017-05-11
Updated: 2017-05-10
Packaged: 2018-10-30 12:05:50
Rating: Explicit
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 1
Words: 3,691
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/10876437
Author URL: https://archiveofourown.org/users/SolaraMoonset/pseuds/SolaraMoonset
Summary: Once, very long ago, Khan save a small group of agument children, his people's hope for the future. When awoken in the future, that hope seems lost. Could three augment children taken from their cryo-tubes early, and raised by humans, mean freedom or damnation for Khan and his people?





	Freedom and Choices

**Author's Note:**

> This is a SLOW BURN! This is also the beginning of a story I have no idea where it's head so ratings / tags / summary may change as the story progress. It's a story about augments, be prepared for violence. I'll throw up a warning before any particular violent scenes (none in either this chapter). As with most of my stories, it takes me forever to update. Let me know what you think of the beginning of this story.
> 
> Disclaimer: I don't own star trek. I don't make profit off of this.

Prolog  
Khan became aware of his surroundings in layers. He was not in his cryo tube; someone must have pulled him out early. He opened his eyes and looked around. The larger room he was in held seventy-two of the cryo pods. Where were the other seventy-seven pods? Kahn ignored the steps in his direction as his glance inventoried the remaining pods.

"Those are all the ones still working. The rest malfunctioned; my crew is working on giving them a space burial. Admiral Alexandar Marcus." Khan turned to the man who spoke. His uniform was unlike anything khan had ever seen before. Khan took the offered hand and shook it.

"Commander Khan Noonien Singh." 

"Walk with me Commander." Khan frowned at the obvious order but stood and followed Marcus through the cryo tubes. “The records from your ship said there was a massive power failure about twenty years ago. Most of the missing pods Failed then, a few shorted out after. You’re from the great augment uprising, correct?”

“Correct.”

“Good. You see you’ve come almost three hundred years into the future, to a civilized age. War is all but forgotten. If we don’t remember, we will be annihilated by our enemies. I figure we can help each other out, I need weapons and you, well you want a safe home for your crew. Now my scientist will help keep those tubes running while you help me. How does that sound?” They had reached the end of the cryo tubes and Marcus was leading him to the door in front of them. Khan had seen the twins sleeping peacefully, but the children were missing. Khan’s steps faltered at the realization; his heart cracked. Marcus turned to look at him an eyebrow rose.

“I will make your weapons.” Khan growled. He couldn’t lose any more of his people. They had already lost their hope for the future, and they didn’t even know it. He would do what he could to keep the rest of his people safe.

“Good. Let’s get you set up in your new lab, Commander. Oh and by the way, Khan Noonien Singh is dead, you’re lieutenant John Harrison now.”

 

~XOX~

 

Mia sat at the bar watching the other recruits around her. Tomorrow they’d be entering the academy. It wasn’t what had been originally planed for them; she almost burst into laughter at that thought. What had been originally planned? She had been built, trained and tortured for a war that had been over for centuries. Jax seemed to sense her humor. Since they had been woken up, they had one thing they never dreamed of, a future that they could choose. As one Jax and Mia turned to Jon; It seemed he was about to start a brawl over one of the other recruits. Mia tilted her head as the man before Jon hit him. He was reckless, and had a daring air about him. Her hand shot out to stop Jax from entering the fray. Jon truly didn’t need their help; his opponent was only human after all. Some of the other recruits jumped to his aid. Just as things got interesting, their commander walked in and ended the show. Oh well, they still needed to come to a decision, stay with Starfleet and pretend to be human for the rest of their lives , or steal a starship to rescue and wake the others. Whatever they choose it would be their decision, and theirs alone. What a priceless freedom. 

“Mia have you decided?” Jon whispered as they left with the recruits. Jax wanted to steal a starship, Jon wanted to join Starfleet. Both had present good reasons why their choice was best, but this choice would be up to Mia. Whatever her decision the others would follow it. Mia looked from one brother to the other. They couldn’t stay with the humans forever, they would start to notice the three siblings were different, but there was no guarantee they’d be able to find the lost ship, or that anyone would still be alive on that ship. There were too many unknowns now to go chasing off into space.

“Better hurry back to the barracks boys, tomorrow we start at the academy.” Mia winked up at her brothers before looping ahead to catch up with some of the female cadets she pretended to befriend. 

 

CH1

“Mia.” Mia tidied up the med lab. After Kirk had managed to chase away half of the nursing staff, Doctor McCoy had begged her to fill in until they could return to earth to pick up some new personnel. Technically she was a science office, at the academy she had also enrolled in the medical program. She was one of six graduates to have graduated with double majors. She was the leading anthropologist on the ship and had nearly the amount of medical training as Dr. McCoy. 

“Yeah doc?” She had been waiting for his page for over an hour now and had a good idea what he wanted. 

“Bring the standard kit down to the brig, we caught the bastard. McCoy out.” Mia turned to the door with kit in had when Jon walked in with a busted lip and a cut bleeding heavily over his eye. Mia arched her eyebrow at him.

“Damn Klingons got a couple hits in. Barnes said I was unconcise.” he muttered.

“You seem to be getting slow in your old age ‘cupcake’. I’ve got to get to the brig, have a seat on one of the bio beds. I’ll be back to fix you in a jiffy.” Mia couldn’t keep the laughter out of her voice as she skipped out the door. Jon’s growl followed her out of the medbay. 

Mia’s humor stayed with her as she turned into the brig. Kirk, Spock and McCoy stood in front of Harrison, blocking him from view. Mia knew she should put the tray down and walk out, but she was curious to see this human who attack so differently, so much more violently, than any others she had meet. 

“Dr. McCoy, the equipment you requested.” Mia called out walking slowly towards the cell. All three of her commanding office turned at her voice, she could see surprise on Kirk and McCoy’s faces. With a playful smirk at McCoy she turned to look at Harrison. Her eyes widened slightly and the tray slipped from her hand to crash to the floor.

“Papa Khan?”

 

~XOX~

 

Khan rolled his eyes at his security detail. They just witnessed he take down over two dozen Klingon warriors and yet they only had two guards take him to the brig. Pathetic. He would play the good prisoner a little while longer. He did need this ship, and its captain for a few more days. Soon the Vengeance would be his, and his crew returned to him. Once in his cell he sat quietly and waited for the captain. The captain did not disappoint, Kirk and his second, Spock came to speak with them. Their doctor, was there as well but Khan payed no attention to him, he wasn’t needed. The main doors to the brig opened, and a soft set of foot falls entered.

“Dr. McCoy, the equipment you requested.” A soft feminine voice, perhaps this one could be turned to his side and help persuade the captain. The men on the other side of his cage turned allowing he a glance at the woman. He caught the playful smirk she shoot at the doctor before looking at him. He noticed his eyes widen and the tray she was holding fell from her grasp. 

“Papa Khan?” he voice was nothing but a whisper, if it hadn’t been for his augment hearing, he never would have heard her. He looked at her, really looked. He had never seen her before, how did she know what the children used to call him, more importantly what did she know of him? His eyes narrowed as the doctor rushed forward and grabbed her arm.

“Mia what is it? You know you should be here.” the doctor started to lead her away as Khan registered what he had called the woman.

“Little Mia?” his brows frowned as she turned to him once again. 

“Lieutenant do you know this man?” The Vulcan glanced between them.

“Yes Commander.” Her voice was soft and khan could see she was in a mild state of shock. 

“Jim, we should continue this elsewhere.” The doctor gently led Mia out. Kirk cast a glance back at him before following the doctor out. At least one of the children had survived and grown up! Khan closed his eyes as he began to rethink his plan.

 

~XOX~

 

Jon jumped to his feet as McCoy led Mia in followed closely by kirk. “What did you do to my sister?” he roared at them grabbing Mia from McCoy’s hold. His hands cupped Mia’s face. “Mia, what is it? Talk to me.”

“He’s alive and … here, on the enterprise.” Her voice was still soft.

“She seems to be in a state of shock. Not sure why a single look at Harrison did that to her. Did you guys have relatives that he killed?” Jim blurted out. McCoy sent him a dirty look.

“No. we’ve got no one left, it’s just her, Jax, and me. It’s been that way for a while. Mia, who’s here?” Jon didn’t look away from Mia.

“Does Papa Khan mean anything to you?” Jon’s head snapped at Spock faster than anyone should have been able to move. His face paled a little.

“What did you say?” he muttered.

“Papa Khan is here.” Mia’s voice brought Jon back to his sense.

“No little Mia, Papa Khan isn’t here. He died a long, long time ago.” Jon pulled Mia into a hug and rocked her gently. Jon glared over her head at their commanding officers. “I don’t know what happened but I’m taking my sister to her quarters.”

“Harrison called her 'little Mia'. it is not a name I have heard you or Jax call her.” Spock said as Jon took a step.

“When we were children, a man maned Khan saved our lives. We lived with him for a time before he was killed. Mia was the one who first thought to call him papa, he in return graced her with 'little Mia' since she was the smallest of us. We haven’t used that name for her in a very long time.” Jon left the med bay quickly as memories he buried long ago began to swim behind his eyes.

 

~XOX~

_  
If it hadn't been for the change in sound Jon would never have known the wall in front of him shook. The scientist that "took care" of them kept their cell dark, there was never any light inside._

_"What are they doing now?" Jax's voice had a slight waver to it._

_"A new experiment." Mia had a waver in her own voice. Blindly she reached her hand out to Jax, finding his hand, she gave it a squeeze._

_"Strength!" Jon hissed at them. Jon was older by about a year, Jax and Mia were only a month apart in age. They were the last experiments left in the facility. The scientists didn't tolerate weakness of any kind. If they had been over heard, Mia and Jax would be beaten for the waver in their voices._

_The wall in front of them cracked spilling light into their prison momentarily blinding them. Jax squeezed Mia's hand quickly before letting go, the scientist always pulled the wall up when it was time for experiments, they'd never broken the wall before. All three jumped to their feet, in defensive stances. More light flooded their cell as the wall exploded inward toward them. A dark shadow, stood on the other side of the wall. He hissed when he saw them, his expression grew dark as he looked around their cell. His dark eyes glowed in rage as he turned from them._

_The scientist always tossed the dead experiments into the back of the cell as a reminder to those left alive what would happen if they failed. No one ever cleaned the cell. Once when there had been older experiments alive, they had attempted to keep the cell clean. Now they were among the dead. The stench must have been horrible, but the three children were used to it._

_The man turned back to them and knelt on the floor outside their cell. " Come here little ones." His voice was gentle, his eyes soften at them. Slowly he reached his hand out to them. The three exchanged a look. No one spoke to them like that, orders were always barked at them. Jon was the first to move forward. Mia was next to leave the cell, the man's touch was gentle, something that she had never felt before._

_"Put those scientists in there and fix this hole." the man growled above their heads. Mia and Jax stood close to Jon. None of them understood what was going one. People growled at them and talked softly to each other, this man was doing the opposite. They could hear the scientists screaming as the man led them away._

_"You are safe now." He called softly down to them._

_"What is safe?" Jax asked. His eyes opened wide and his hands streaked up to his mouth. Instantly Mia shoved Jax behind her and Jon. Both took defensive stances in front of him. Questions were never tolerated and met with severe punishment. The man frowned at their actions. slowly, so not to startle them he knelt to their level._

_"No one will hurt you again. You can ask questions, you can speak your mind. if you don't like something you can tell us. You will never be used as lab experiments again. This is the start of what safe means for us." his voice was once again gentle. Mia's stance relaxed._

_"Who are you?"_

_"Khan Noonien Singh. What are your names?"_

_"They called us, 279, 323, and 324." Jon answered. Khan frowned._

_"Those are not names." Mia took a slow step forward until she was standing in front of Jon._

_"Before she died Bridgette gave us different names. I'm Mia, this is Jax and that's Jon." she timidly answered. Khan smiled at her._

_"It's nice to meet you Mia."  
_

~XOX~

_Two years had pasted and the war with the humans ragged on. The augments were losing, the last of their people were hand taken control of a rocket assembly plant and were building a ship to hopefully take them into space. Mia, Jax and Jon were the only augment child to be found alive and they were cherished by their people. It had been discovered that the female augments were unable to conceive and the men would not lower themselves to breed with humans._  
  
_Mia sat at the base of Khan's throne as he studied escape plans, trying to decide which would save the most of his people. Her brothers, as they were called, were reading a few feet away. The twins Joachim and Joaquin rushed in as the room shook violently._  
  
_"Commander, we're out of time!" Quin called. Khan grabbed Mai and headed to the back escape._  
  
_"Grab the boys, hit the alarm, and pray the ship is ready." Khan led the way to the hanger, augments streamed in from every doorway._  
  
_"Get aboard and into cryo!” Khan ordered racing to the bridge of the ship. he placed Mai down in the co-pilot’s seat, sitting in the pilot’s seat and began the launch sequence. Mia watched spell bounded as Khan’s hands flew across the controls. She buckled the straps around her as she had seen Kahn do._  
  
_"We're set commander!" Chim ran onto the bridge. Khan nodded once but didn't look up from the controls. the ship shook and lurched to the side as it lifted off the ground. Chim was thrown into the wall behind them. the sky opened before them, laser blasts peppered the sky; soon the bright blue gave way to an inky blackness and the laser blasts stopped._  
  
_" Papa Khan, will our new home be safe?" Mia asked as they left Earth's orbit._  
  
_"I hope so. Now let’s get you into cryo. Chim." Khan called over his shoulder. Mia unbuckled and hugged Khans leg before heading over to Chim. Chim took Mia's hand leading her away as Khan continued to piolet the ship._  
  
_“Good night Papa.” Mia called. Khan’s hands stopped and he glanced back at the empty doorway. He would keep them safe, if for no other reason than to be the man Mia and her brothers thought him to be. He sighed as he resumed his worked, he loved that little girl, and the light she brought into his life._

~XOX~ 

_Mia sat up gasping for air. Her eyes flew open, in front of her was someone she'd never seen before. He looked down at her curiously. His hand rubbing gentle circles on her back._  
  
_“Breath little one, just breath.”_  
  
_"Doctor Stephens we've got a couple more kids over here. Looks like their pods are failing too." a voice called. Mia tried to look in that directions but this Doctor Stephens was blocking her view. Khan had said he’d protect her from doctors and scientists. Where was her papa? Who were these people?_  
  
_“Papa?” Mia crocaked. Doctor Stephens’ expression grew grim._  
  
_"Get them outta there! Ensign, get these Kids to the med bay." Doctor Stephens ordered._  
  
_"Yes sir, but what about the rest of the pods?" the voice called again._  
  
_"If they're failing get the people out of them, if not, leave them. We don't have room or supplies to wake everyone up."_  
  
_"And the dead sir?"_  
  
_"Leave them. We can't give them a proper funereal anyway."_  
  
_“PAPA!” Mia called again, this time louder. Doctor Stephens pulled her from the pod and held her like Khan had during the escape._  
  
_“Hush sweetie, you’re safe now.” On the way out Mia saw Khan’s sleeping face. She reached out her arm towards him._  
  
_“PAPA! WAKE UP!” Khan’s form didn’t move._

~XOX~ 

Mia looked up at the sound of a chime. She had been reliving the three best and simultaneously worst days of her life. Jon was at her door letting the captain in. Spock, McCoy, and Jax were with him. “You want answers.” Her voice was steadier and louder than it had been since seeing Khan.  
  
“You seem better.” Kirk smirked at her as McCoy began checking her vitals.  
  
“I received a nasty shock. I’m fine now. Doctor McCoy stop.” Her voice turned cold, McCoy stepped away, having never heard her use that tone before.  
  
“Mia, I don’t think it’s a good idea-” Jax began.  
  
“We not who you think we are. We were genetic experiments created in a lab. The man claiming to be our father, Doctor Edward Stephens, found us in space nearly twenty years ago. We were cryogenically frozen, along with one hundred and forty-seven others, while attempting to flee earth three hundred years ago. Doctor Stephens found our ship as our cryo pods were failing. He saved myself, and my brothers, but left everyone else to die in their sleep. That man in the bring is our father, one that we believed dead. I now question what else Doctor Stephens told us.” Mia cut Jax off. Kirk gave her an odd look before laughing.  
“Out of everything we thought about how you would know Harrison, I can honestly nothing like that occurred to us.” Jon and Jax looked at Kirk.  
  
“Wait you believe that? We don’t have to prove it?” Jax blurted out.  
  
“I found irregulates in Mia’s blood before.” McCoy said offhandedly.  
  
“And Cupcake hits at least as hard as a Vulcan. humans just don’t have that kind of strength.” Kirk added.  
  
“It was illogical to push you into telling us about what seemed to be a minor glitch in your family records when you preform your duties above and beyond expectation. Now we are face with the decision of what to do with this knowledge and how this will effect Harrison’s trail.”  
  
“I don’t know how he woke up, or when but you have to believe me, my father wouldn’t open fire on a room full of people, or blow up an archive for no reason. We’re missing something.” Mia looked at Jax who nodded.  
  
“Like if he’s alive, where’s the rest of our family?” Jon leaned against the wall.  
  
“I understand you have questions, but you remember we’re taking him back to face murder charges? He is a criminal. He killed several people, including admiral Pike.” Kirk’s laughter had disappeared, his face set in hard lines.  
  
“But Jim, we don’t know why. Let us talk to him.” Mia blinked in surprise, she had not planned on asking Kirk to see Khan again.  
  
“at least let us ask him about the others.” Jon added.  
  
“we don’t need any extra time, we can talk with him on the journey back to earth.” Jax piped up.  
  
“No way.” Kirk shook his head.  
  
“Captain, he may open up and tell them the truth. There are many questions still unanswered.”  
  
“Not you too Spock.”  
  
“Jim, they have a point.”  
  
“Dammit Bones! He’s a killer and you want to send Mia in there with him?” Mia looked startled at Kirk’s statement.  
  
“I’m not asking to be let in the cell, nor am I asking to go alone.” Mia said softly.  
  
“I don’t care what happened to him, Khan would never hurt Mia. he used to spoil her as much as possible.” Jon’s eyes seemed to be looking into the past.  
  
“She was his little princess.” Smirked Jax. Mia gave him a nasty look.  
  
“I’m not fond of being called a princess.” Mia’s glare at Jax increased. Kirk’s eyebrows rose at that.  
  
“Really? Tell you what princess, you can go stand outside Harrison’s cell, with Cupcake and Jax if and only if Spock or I are with you.” Kirk smirked down at Mia.  
  
“Oh, god Jim, don’t you start!” Mia’s dropped her face into her hands. 

“We’ll do it.” Jon added. 

**Author's Note:**

> Love it? Hate it? Thought it was just meh? Let me know!


End file.
